The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo-and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.

The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.

Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.ConclusionsThis paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.Graphical abstractCDK 2.0 provides new features and improved performance Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.

The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemoand Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as access information for interested users and potential contributors are given.

BackgroundSince 2009, IPF patients across Europe are recruited into the eurIPFreg, providing epidemiological data and biomaterials for translational research.MethodsThe registry data are based on patient and physician baseline and follow-up questionnaires, comprising 1700 parameters. The mid- to long-term objectives of the registry are to provide clues for a better understanding of IPF phenotype sub-clusters, triggering factors and aggravating conditions, regional and environmental characteristics, and of disease behavior and management.ResultsThis paper describes baseline data of 525 IPF subjects recruited from 11/2009 until 10/2016. IPF patients had a mean age of 68.1 years, and seeked medical advice due to insidious dyspnea (90.1%), fatigue (69.2%), and dry coughing (53.2%). A surgical lung biopsy was performed in 32% in 2009, but in only 8% of the cases in 2016, possibly due to increased numbers of cryobiopsy. At the time of inclusion in the eurIPFreg, FVC was 68.4% ± 22.6% of predicted value, DLco ranged at 42.1% ± 17.8% of predicted value (mean value ± SD). Signs of pulmonary hypertension were found in 16.8%. Steroids, immunosuppressants and N-Acetylcysteine declined since 2009, and were replaced by antifibrotics, under which patients showed improved survival (p = 0.001).ConclusionsOur data provide important insights into baseline characteristics, diagnostic and management changes as well as outcome data in European IPF patients over time.Trial registrationThe eurIPFreg and eurIPFbank are listed in ClinicalTrials.gov(NCT02951416).

Optically levitated nano-objects in vacuum are amongst the highest-quality mechanical oscillators, and thus of great interest for force sensing, cavity quantum optomechanics, and nanothermodynamic studies. These precision applications require exquisite control. Here, we present full control over the rotational and translational dynamics of an optically levitated silicon nanorod. We trap its centre-ofmass and align it along the linear polarization of the laser field. The rod can be set into rotation at a predefined frequency by exploiting the radiation pressure exerted by elliptically polarized light. The rotational motion of the rod dynamically modifies the optical potential, which allows tuning of the rotational frequency over hundreds of Kilohertz. Through nanofabrication, we can tailor all of the trapping frequencies and the optical torque, achieving reproducible dynamics which are stable over months, and analytically predict the motion with great accuracy. This first demonstration of full ro-translational control of nanoparticles in vacuum opens up the fields of rotational optomechanics, rotational ground state cooling and the study of rotational thermodynamics in the underdamped regime.

Laser cooling has given a boost to atomic physics throughout the last 30 years, as it allows one to prepare atoms in motional states, which can only be described by quantum mechanics. Most methods rely, however, on a near-resonant and cyclic coupling between laser light and well-defined internal states, which has remained a challenge for mesoscopic particles. An external cavity may compensate for the lack of internal cycling transitions in dielectric objects and it may provide assistance in the cooling of their centre-of-mass state. Here we demonstrate cavity cooling of the transverse kinetic energy of silicon nanoparticles freely propagating in high vacuum (<10−8 mbar). We create and launch them with longitudinal velocities down to v≤1 m s−1 using laser-induced ablation of a pristine silicon wafer. Their interaction with the light of a high-finesse infrared cavity reduces their transverse kinetic energy by up to a factor of 30.

Nanomechanical devices have attracted the interest of a growing interdisciplinary research community, since they can be used as highly sensitive transducers for various physical quantities. Exquisite control over these systems facilitates experiments on the foundations of physics. Here, we demonstrate that an optically trapped silicon nanorod, set into rotation at MHz frequencies, can be locked to an external clock, transducing the properties of the time standard to the rod’s motion with a remarkable frequency stability f r/Δf r of 7.7 × 1011. While the dynamics of this periodically driven rotor generally can be chaotic, we derive and verify that stable limit cycles exist over a surprisingly wide parameter range. This robustness should enable, in principle, measurements of external torques with sensitivities better than 0.25 zNm, even at room temperature. We show that in a dilute gas, real-time phase measurements on the locked nanorod transduce pressure values with a sensitivity of 0.3%.